FF:12124-128C9: Difference between revisions

Revision as of 09:56, 28 November 2014

Name:	stem cell (cKit+ Sca1- lineage-) KSL, biol_rep2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12535
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/8J
tissue	bone marrow
dev stage	NA
sex	male
age	9-10weeks
cell type	stem cell (cKit+ Sca1- lineage-)
cell line	NA
company	NA
collaboration	Kitamura/Nakahara
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	rep2
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005977

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12535		CAGE		DRX008785		DRR009657

Accession ID Mm9

Library id		BAM		CTSS
CNhs12535		DRZ001082		DRZ002467

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} donwload]

Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.

Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. Analyst:NA link to dataset. data

CNhs12535

0	0
1	0
10	0
100	0
1000	-0.00703
1001	-0.0631
1002	-0.116
1003	-0.111
1004	0
1005	0.0569
1006	-0.143
1007	-0.17
1008	0
1009	-0.0804
101	0.254
1010	0
1011	0.0569
1012	0
1013	-0.169
1014	-0.0851
1015	0.00923
1016	-0.266
1017	0
1018	0.107
1019	0
102	0.107
1020	0
1021	0
1022	-0.0704
1023	0.76
1024	0.979
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0887
1030	0
1031	-0.854
1032	-0.184
1033	0.199
1034	0
1035	0
1036	0.464
1037	0
1038	-0.241
1039	-0.102
104	0
1040	-0.121
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression Analyst: Michiel de Hoon link to dataset. data

library id: CNhs12535

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.63896e-7
MA0003.1	MA0003.1	0.763
MA0004.1	MA0004.1	0.211
MA0006.1	MA0006.1	0.88
MA0007.1	MA0007.1	0.833
MA0009.1	MA0009.1	0.273
MA0014.1	MA0014.1	0.871
MA0017.1	MA0017.1	0.337
MA0018.2	MA0018.2	1.68121e-11
MA0019.1	MA0019.1	0.601
MA0024.1	MA0024.1	7.39556e-4
MA0025.1	MA0025.1	5.0228e-4
MA0027.1	MA0027.1	0.0391
MA0028.1	MA0028.1	2.88778e-8
MA0029.1	MA0029.1	0.384
MA0030.1	MA0030.1	0.247
MA0031.1	MA0031.1	0.00385
MA0035.2	MA0035.2	0.917
MA0038.1	MA0038.1	0.00607
MA0039.2	MA0039.2	0.244
MA0040.1	MA0040.1	0.0286
MA0041.1	MA0041.1	0.504
MA0042.1	MA0042.1	0.532
MA0043.1	MA0043.1	1.57493e-7
MA0046.1	MA0046.1	5.93308e-15
MA0047.2	MA0047.2	0.579
MA0048.1	MA0048.1	0.0229
MA0050.1	MA0050.1	1.3056e-15
MA0051.1	MA0051.1	2.52363e-9
MA0052.1	MA0052.1	0.396
MA0055.1	MA0055.1	0.0278
MA0057.1	MA0057.1	0.764
MA0058.1	MA0058.1	0.087
MA0059.1	MA0059.1	0.103
MA0060.1	MA0060.1	0.357
MA0061.1	MA0061.1	4.15816e-13
MA0062.2	MA0062.2	1.93427e-22
MA0065.2	MA0065.2	0.756
MA0066.1	MA0066.1	0.275
MA0067.1	MA0067.1	1.17581e-5
MA0068.1	MA0068.1	0.0132
MA0069.1	MA0069.1	0.628
MA0070.1	MA0070.1	0.669
MA0071.1	MA0071.1	0.926
MA0072.1	MA0072.1	0.592
MA0073.1	MA0073.1	0.647
MA0074.1	MA0074.1	0.778
MA0076.1	MA0076.1	3.46685e-8
MA0077.1	MA0077.1	0.325
MA0078.1	MA0078.1	0.947
MA0079.2	MA0079.2	0.432
MA0080.2	MA0080.2	2.5526e-14
MA0081.1	MA0081.1	2.12769e-5
MA0083.1	MA0083.1	0.515
MA0084.1	MA0084.1	0.142
MA0087.1	MA0087.1	0.99
MA0088.1	MA0088.1	0.483
MA0090.1	MA0090.1	0.00583
MA0091.1	MA0091.1	0.285
MA0092.1	MA0092.1	0.276
MA0093.1	MA0093.1	0.16
MA0099.2	MA0099.2	4.06301e-24
MA0100.1	MA0100.1	0.00397
MA0101.1	MA0101.1	7.08398e-18
MA0102.2	MA0102.2	0.0197
MA0103.1	MA0103.1	0.131
MA0104.2	MA0104.2	0.0965
MA0105.1	MA0105.1	2.18381e-6
MA0106.1	MA0106.1	0.722
MA0107.1	MA0107.1	5.45564e-20
MA0108.2	MA0108.2	0.482
MA0111.1	MA0111.1	0.8
MA0112.2	MA0112.2	0.874
MA0113.1	MA0113.1	0.762
MA0114.1	MA0114.1	0.012
MA0115.1	MA0115.1	0.782
MA0116.1	MA0116.1	0.0621
MA0117.1	MA0117.1	0.0041
MA0119.1	MA0119.1	0.0568
MA0122.1	MA0122.1	0.131
MA0124.1	MA0124.1	0.994
MA0125.1	MA0125.1	0.0686
MA0131.1	MA0131.1	0.167
MA0135.1	MA0135.1	0.843
MA0136.1	MA0136.1	2.51251e-30
MA0137.2	MA0137.2	0.00259
MA0138.2	MA0138.2	1.8912e-5
MA0139.1	MA0139.1	0.892
MA0140.1	MA0140.1	0.698
MA0141.1	MA0141.1	0.0941
MA0142.1	MA0142.1	0.518
MA0143.1	MA0143.1	0.0498
MA0144.1	MA0144.1	0.0638
MA0145.1	MA0145.1	0.461
MA0146.1	MA0146.1	0.1
MA0147.1	MA0147.1	0.112
MA0148.1	MA0148.1	0.988
MA0149.1	MA0149.1	0.339
MA0150.1	MA0150.1	2.87117e-7
MA0152.1	MA0152.1	0.859
MA0153.1	MA0153.1	1.8033e-5
MA0154.1	MA0154.1	0.833
MA0155.1	MA0155.1	0.335
MA0156.1	MA0156.1	1.23664e-27
MA0157.1	MA0157.1	0.0265
MA0159.1	MA0159.1	0.455
MA0160.1	MA0160.1	0.746
MA0162.1	MA0162.1	0.592
MA0163.1	MA0163.1	0.00257
MA0164.1	MA0164.1	0.745
MA0258.1	MA0258.1	0.447
MA0259.1	MA0259.1	0.358

FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above Analyst: Michiel de Hoon link to dataset. data

library id: CNhs12535

Novel motif	Logo	P-value
1	1	0.872
10	10	0.234
100	100	0.969
101	101	0.465
102	102	0.84
103	103	0.411
104	104	0.582
105	105	0.525
106	106	0.0695
107	107	0.689
108	108	0.623
109	109	0.642
11	11	0.966
110	110	0.606
111	111	0.968
112	112	0.27
113	113	0.797
114	114	0.0998
115	115	0.624
116	116	0.631
117	117	2.17724e-4
118	118	0.176
119	119	0.611
12	12	0.472
120	120	0.366
121	121	0.263
122	122	0.545
123	123	0.163
124	124	0.336
125	125	0.945
126	126	0.53
127	127	0.876
128	128	0.208
129	129	0.892
13	13	0.00308
130	130	0.57
131	131	0.211
132	132	0.391
133	133	0.257
134	134	0.907
135	135	0.697
136	136	0.0908
137	137	0.00684
138	138	0.973
139	139	0.6
14	14	0.573
140	140	0.698
141	141	0.557
142	142	0.503
143	143	0.247
144	144	0.845
145	145	0.499
146	146	0.668
147	147	0.49
148	148	0.361
149	149	0.175
15	15	0.195
150	150	0.818
151	151	0.744
152	152	0.156
153	153	0.329
154	154	0.571
155	155	0.523
156	156	0.292
157	157	0.748
158	158	0.0336
159	159	0.702
160	160	0.0839
161	161	0.435
162	162	0.515
163	163	0.0437
164	164	0.0542
165	165	0.136
166	166	0.215
167	167	0.535
168	168	0.156
169	169	0.192
17	17	0.845
18	18	0.956
19	19	0.0758
2	2	0.0168
20	20	0.0228
21	21	0.957
22	22	0.995
23	23	0.402
24	24	0.0869
25	25	0.559
26	26	0.0935
27	27	0.382
28	28	0.687
29	29	0.271
3	3	0.638
30	30	0.191
31	31	0.444
32	32	0.0382
33	33	0.146
34	34	0.653
35	35	0.944
36	36	0.2
37	37	0.0583
38	38	0.676
39	39	0.364
4	4	0.488
40	40	0.314
41	41	0.114
42	42	0.66
43	43	0.871
44	44	0.983
45	45	0.7
46	46	0.986
47	47	0.642
48	48	0.682
49	49	0.949
5	5	0.868
50	50	0.62
51	51	0.609
52	52	0.606
53	53	0.803
54	54	0.551
55	55	0.995
56	56	0.963
57	57	0.535
58	58	0.342
59	59	0.696
6	6	0.786
60	60	0.537
61	61	0.368
62	62	0.395
63	63	0.552
64	64	0.641
65	65	0.97
66	66	0.431
67	67	0.779
68	68	0.436
69	69	0.574
7	7	0.69
70	70	0.562
71	71	0.261
72	72	0.453
73	73	0.0329
74	74	0.569
75	75	0.00883
76	76	0.115
77	77	0.00552
78	78	0.352
79	79	0.596
8	8	0.899
80	80	0.746
81	81	0.792
82	82	0.163
83	83	0.00591
84	84	0.552
85	85	0.087
86	86	0.225
87	87	0.0105
88	88	0.414
89	89	0.233
9	9	0.727
90	90	0.535
91	91	0.403
92	92	0.439
93	93	0.153
94	94	0.789
95	95	0.00349
96	96	0.376
97	97	0.92
98	98	0.604
99	99	0.026

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown. Analyst:NA library id: CNhs12535

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000021 hematopoietic stem cell sample
FF:0000103 mouse sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000021 (hematopoietic stem cell sample)
0000103 (mouse sample)
0000001 (sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
NA

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr7:19895354..19895369,-!p1@Fosb!2.75!759.52!Fosb;;chr7:19895384..19895399,-!p2@Fosb!2.37!326.65!Fosb;;chr15:101097270..101097290,+!p1@Nr4a1!2.34!2085.42!Nr4a1;;chr1:193007123..193007139,-!p1@Atf3!2.16!757.98!Atf3;;chr4:124805061..124805087,-!p1@Zc3h12a!1.93!248.97!Zc3h12a;;chr1:38721792..38721845,-!p1@Aff3!1.93!103.42!Aff3;;chr11:16908650..16908690,-!p1@Plek!1.80!362.47!Plek;;chr7:31206743..31206761,+!p1@Nfkbid!1.80!84.53!Nfkbid;;chr16:55838757..55838774,-!p2@Nfkbiz!1.79!70.82!Nfkbiz;;chr12:86814833..86814846,+!p1@Fos!1.78!1278.04!Fos;;chr8:87502608..87502623,-!p1@Junb!1.68!713.33!Junb;;chr16:92826249..92826325,-!p1@Runx1!1.65!103.28!Runx1;;chr11:23670750..23670789,-!p2@Rel!1.56!65.50!Rel;;chr19:5447886..5447905,+!p1@Fosl1!1.56!34.99!Fosl1;;chr4:48058129..48058179,+!p2@Nr4a3!1.53!60.60!Nr4a3;;chr11:11586218..11586285,+!p1@Ikzf1!1.50!95.59!Ikzf1;;chr5:140267510..140267555,+!p2@Mafk!1.49!69.00!Mafk;;chr6:52176164..52176195,-!p1@Hoxa9!1.49!37.09!Hoxa9;;chr2:90936978..90937023,+!p3@Sfpi1!1.47!53.46!Sfpi1;;chr1:52065508..52065522,+!p2@Stat4!1.46!32.75!Stat4;;chr13:59923965..59924003,-!p2@Zcchc6!1.45!32.19!Zcchc6;;chr17:44873258..44873281,-!p5@Runx2!1.44!34.85!Runx2;;chr16:55822241..55822258,-!p1@Nfkbiz!1.43!773.79!Nfkbiz;;chr2:56967334..56967366,-!p1@Nr4a2!1.43!52.06!Nr4a2;;chr2:90936901..90936945,+!p1@Sfpi1!1.42!129.32!Sfpi1;;chr4:134708451..134708469,+!p1@Runx3!1.42!44.36!Runx3;;chr5:92391466..92391471,+!p2@Thap6!1.42!36.39!Thap6;;chr4:94718861..94718872,-!p2@Jun!1.41!177.04!Jun;;chr17:44872561..44872615,-!p1@Runx2!1.40!54.16!Runx2;;chr19:5447692..5447711,+!p2@Fosl1!1.40!23.93!Fosl1;;chr2:90936947..90936977,+!p2@Sfpi1!1.39!45.90!Sfpi1;;chr7:19895546..19895577,-!p3@Fosb!1.39!23.65!Fosb;;chr10:20880629..20880683,-!p1@Myb!1.37!62.98!Myb;;chr1:52065454..52065495,+!p1@Stat4!1.37!36.39!Stat4;;chr7:31208285..31208312,+!p3@Nfkbid!1.36!23.93!Nfkbid;;chr3:135354384..135354443,-!p1@Nfkb1!1.35!125.68!Nfkb1;;chr14:79915425..79915501,+!p1@Elf1!1.32!170.46!Elf1;;chr15:25914235..25914246,+!p5@Zfp622!1.32!19.73!Zfp622;;chr4:48058016..48058032,+!p3@Nr4a3!1.31!32.61!Nr4a3;;chr13:5860776..5860796,+!p1@Klf6!1.30!437.91!Klf6;;chr11:23670953..23671028,-!p1@Rel!1.26!96.29!Rel;;chr7:31207408..31207450,+!p4@Nfkbid!1.26!27.99!Nfkbid;;chr12:56593574..56593592,-!p1@Nfkbia!1.25!834.25!Nfkbia;;chr11:53583544..53583559,+!p1@Irf1!1.25!274.86!Irf1;;chr4:55545337..55545357,-!p1@Klf4!1.25!241.70!Klf4;;chr15:79177964..79177986,+!p1@Maff!1.25!56.54!Maff;;chr19:5637528..5637548,+!p2@Rela!1.24!94.19!Rela;;chr6:108610428..108610440,+!p4@Bhlhe40!1.23!22.11!Bhlhe40;;chr1:36364590..36364608,+!p1@Arid5a!1.22!156.61!Arid5a;;chr18:3281750..3281776,-!p2@Crem!1.22!31.07!Crem;;chr7:19895122..19895142,-!p4@Fosb!1.22!15.53!Fosb;;chr4:94718879..94718898,-!p1@Jun!1.21!1074.97!Jun;;chr19:12871064..12871095,-!p2@Zfp91!1.21!15.11!Zfp91;;chr3:135271185..135271254,-!p4@Nfkb1!1.20!26.73!Nfkb1;;chr15:38230448..38230470,-!p1@Klf10!1.19!296.14!Klf10;;chr6:53523358..53523388,+!p1@Creb5!1.19!170.74!Creb5;;chr17:45692676..45692695,+!p2@Nfkbie!1.19!29.39!Nfkbie;;chr13:83663902..83663927,+!p1@Mef2c!1.18!333.92!Mef2c;;chr11:90252223..90252240,-!p1@Hlf!1.17!113.50!Hlf;;chr13:5860872..5860883,+!p3@Klf6!1.17!27.71!Klf6;;chr19:43686789..43686811,+!p1@Nkx2-3!1.16!13.44!Nkx2-3;;chr10:20880731..20880775,-!p2@Myb!1.15!27.71!Myb;;chr8:74842952..74842970,+!p1@Klf2!1.14!855.94!Klf2;;chr11:100683839..100683890,-!p2@Stat5b!1.14!29.67!Stat5b;;chr17:45692642..45692663,+!p1@Nfkbie!1.13!39.47!Nfkbie;;chr15:103085802..103085817,-!p4@Nfe2!1.13!15.81!Nfe2;;chr19:46379199..46379301,+!p1@Nfkb2!1.12!69.00!Nfkb2;;chr15:38230415..38230426,-!p2@Klf10!1.12!42.41!Klf10;;chr4:48058047..48058062,+!p1@Nr4a3!1.12!18.61!Nr4a3;;chr15:79178060..79178074,+!p2@Maff!1.12!15.81!Maff;;chr3:30993974..30994045,+!p1@Skil!1.11!327.49!Skil;;chr7:20214704..20214800,-!p1@Relb!1.11!38.91!Relb;;chr14:79915502..79915514,+!p4@Elf1!1.11!18.33!Elf1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.11!15.39!Zbtb11;;chr14:79915521..79915539,+!p5@Elf1!1.11!14.28!Elf1;;chr18:75527210..75527215,+!p4@Smad7!1.10!20.01!Smad7;;chr18:35020854..35020869,+!p1@Egr1!1.09!433.85!Egr1;;chr7:71083729..71083742,-!p4@Klf13!1.09!20.15!Klf13;;chr19:37509324..37509337,+!p1@Hhex!1.08!77.53!Hhex;;chr1:52065530..52065548,+!p3@Stat4!1.08!10.92!Stat4;;chr4:124805092..124805135,-!p2@Zc3h12a!1.07!46.04!Zc3h12a;;chr6:99216488..99216534,-!p2@Foxp1!1.07!30.93!Foxp1;;chr6:52163319..52163342,-!p1@Hoxa3!1.07!15.67!Hoxa3;;chr17:51971932..51971958,-!p2@Satb1!1.06!14.55!Satb1;;chr1:193041811..193041838,-!p2@Atf3!1.06!10.36!Atf3;;chr5:22940353..22940372,+!p3@Mll5!1.03!19.17!Mll5;;chr15:25914217..25914232,+!p3@Zfp622!1.03!18.75!Zfp622;;chr15:79178029..79178044,+!p4@Maff!1.03!12.04!Maff;;chr11:100800641..100800669,-!p3@Stat3!1.02!16.79!Stat3;;chr8:73222425..73222444,+!p2@Jund!1.02!9.38!Jund;;chr6:108610610..108610676,+!p1@Bhlhe40!1.01!457.64!Bhlhe40;;chr16:95680889..95680991,-!p1@Erg!1.01!75.99!Erg;;chr6:133986042..133986052,+!p7@Etv6!1.01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@@ Line 44: / Line 44: @@
 |is_obsolete=
 |library_id=CNhs12535
-|library_id_phase_based=1:CNhs12535
+|library_id_phase_based=2:CNhs12535
 |name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep2
 |namespace=FANTOM5
@@ Line 50: / Line 50: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12535,LSID920,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0.056886356216389,0,-0.174964349979897,0,0,0,0,-0.0274528841801525,0,0,0,0,0.11519345261068,0,-0.0847163262154184,0,0.148295322256383,0,0,0,0,0,0,0,0,0,0,0,-0.23216650090268,0,0,0,0,0,-0.036665559523882,-0.0810199640178311,-0.0813100747001601,-0.984211366477826,0.201323340033329,0.056886356216389,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.056886356216389,0,0.0175987568055965,0,0.107177024667156,0,-0.117389802908326,0.160541320704294,-0.101204686554694,-0.0586559928255204,0,0,-0.0672592169170953,0,0.354024468246181,0,-0.0445577358621875,-0.175569308430604,-0.59591488074057,-0.0788315948399074,0,0,0,0,0,0,-0.268029527476267,-0.895264133183884,-0.269803002231399,0,0,0,0,0

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FF:12124-128C9: Difference between revisions

From FANTOM5_SSTAR

Revision as of 09:56, 28 November 2014

CNhs12535

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0